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FreeBSD Ports: Biology

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Software related to biology.

InsightToolkit-2.8.1_2
Insight Toolkit
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: cmake-2.8.9, cmake-modules-2.8.9
Also listed in: Science

adun-0.81_1
Molecular Simulator for GNUstep
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: aspell-0.60.6.1_2, cups-client-1.5.2_2, damageproto-1.2.1, dri2proto-2.6, expat-2.0.1_2, fixesproto-5.0, flac-1.2.1_3, fontconfig-2.9.0,1, freetype2-2.4.9_1, gettext-0.18.1.1, giflib-4.2.0_2, gmake-3.82_1, gmp-5.0.5, gnustep-back-0.22.0, gnustep-base-1.24.0, gnustep-gui-0.22.0, gnustep-make-2.6.2, gnutls-2.12.18_1, gsl-1.15_1, jbigkit-1.6, jpeg-8_3, kbproto-1.0.5, libGL-7.6.1_2, libGLU-7.6.1_1, libICE-1.0.7,1, libSM-1.2.0,1, libX11-1.4.4,1, libXau-1.0.6, libXdamage-1.1.3, libXdmcp-1.1.0, libXext-1.3.0_1,1, libXfixes-5.0, libXft-2.1.14, libXmu-1.1.0,1, libXrender-0.9.6, libXt-1.1.1,1, libXxf86vm-1.1.1, libao-1.1.0_1, libdrm-2.4.17_1, libffi-3.0.9, libgcrypt-1.5.0_1, libgpg-error-1.10, libiconv-1.14, libogg-1.3.0,4, libpciaccess-0.12.1, libpthread-stubs-0.3_3, libsndfile-1.0.25_2, libvorbis-1.3.3_1,3, libxcb-1.7, libxml2-2.7.8_5, libxslt-1.1.26_3, mDNSResponder-333.10, nettle-2.5, p11-kit-0.14, pciids-20120906, pkgconf-0.8.9, png-1.5.12, renderproto-0.11.1, tiff-4.0.2_1, xextproto-7.2.0, xf86vidmodeproto-2.3.1, xproto-7.0.22
Also listed in: Gnustep

afni-2012.04.17.2129_1
Advanced Functional Neuro Imaging
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: R-2.15.1_1, bash-4.2.37, binutils-2.22_3, bitstream-vera-1.10_5, cairo-1.10.2_4,2, cups-client-1.5.2_2, cups-image-1.5.2_1, damageproto-1.2.1, dri2proto-2.6, encodings-1.0.4,1, endian-1.0, expat-2.0.1_2, fixesproto-5.0, font-bh-ttf-1.0.3, font-misc-ethiopic-1.0.3, font-misc-meltho-1.0.3, font-util-1.2.0, fontconfig-2.9.0,1, freetype2-2.4.9_1, gamin-0.1.10_4, gcc-4.6.3, gettext-0.18.1.1, ghostscript9-9.06_1, gio-fam-backend-2.28.8_1, glib-2.28.8_4, gmake-3.82_1, gmp-5.0.5, gobject-introspection-0.10.8_2, gsfonts-8.11_5, gsl-1.15_1, icu-4.8.1.1_1, inputproto-2.0.2, jasper-1.900.1_10, jbig2dec-0.11_1, jbigkit-1.6, jpeg-8_3, kbproto-1.0.5, lcms2-2.4, libGL-7.6.1_2, libGLU-7.6.1_1, libGLw-7.6.1_1, libICE-1.0.7,1, libSM-1.2.0,1, libX11-1.4.4,1, libXau-1.0.6, libXaw-1.0.9,2, libXdamage-1.1.3, libXdmcp-1.1.0, libXext-1.3.0_1,1, libXfixes-5.0, libXft-2.1.14, libXi-1.4.5,1, libXmu-1.1.0,1, libXp-1.0.1,1, libXpm-3.5.9, libXrender-0.9.6, libXt-1.1.1,1, libXxf86vm-1.1.1, libdrm-2.4.17_1, libffi-3.0.9, libfontenc-1.1.0, libiconv-1.14, libidn-1.25, libpaper-1.1.24_1, libpciaccess-0.12.1, libpthread-stubs-0.3_3, libxcb-1.7, libxml2-2.7.8_5, mkfontdir-1.0.6, mkfontscale-1.0.9, mpc-0.9, mpeg_encode-1.5b, mpfr-3.1.1, netpbm-10.35.86, open-motif-2.3.4, pango-1.28.4_1, pciids-20120906, pcre-8.31_1, perl-5.14.2_2, pixman-0.24.2, pkgconf-0.8.9, png-1.5.12, printproto-1.0.5, python27-2.7.3_3, renderproto-0.11.1, svgalib-1.4.3_6, tcl-8.5.12_2, tcl-modules-8.5.12_2, tiff-4.0.2_1, tk-8.5.12, whirlgif-3.04, xbitmaps-1.1.1, xcb-util-0.3.8,1, xcb-util-renderutil-0.3.8, xextproto-7.2.0, xf86vidmodeproto-2.3.1, xorg-fonts-truetype-7.5.1, xproto-7.0.22
Also listed in: Science, Graphics

ariadne-1.3
Programs to compare protein sequences and profiles
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: gettext-0.18.1.1, gmake-3.82_1, libiconv-1.14

artemis-9_1
A DNA sequence viewer and annotation tool
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: dejavu-2.33, expat-2.0.1_2, fontconfig-2.9.0,1, freetype2-2.4.9_1, inputproto-2.0.2, java-zoneinfo-2012.h, javavmwrapper-2.4_2, jpeg-8_3, kbproto-1.0.5, libICE-1.0.7,1, libSM-1.2.0,1, libX11-1.4.4,1, libXau-1.0.6, libXaw-1.0.9,2, libXdmcp-1.1.0, libXext-1.3.0_1,1, libXft-2.1.14, libXi-1.4.5,1, libXmu-1.1.0,1, libXp-1.0.1,1, libXpm-3.5.9, libXrender-0.9.6, libXt-1.1.1,1, libXtst-1.2.0, libiconv-1.14, libpthread-stubs-0.3_3, libxcb-1.7, open-motif-2.3.4, openjdk6-b27, pkgconf-0.8.9, png-1.5.12, printproto-1.0.5, recordproto-1.14.1, renderproto-0.11.1, xbitmaps-1.1.1, xextproto-7.2.0, xproto-7.0.22
Also listed in: Java

avida-2.12.4
An auto-adaptive genetic system designed for ALife research
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: cmake-2.8.9, cmake-modules-2.8.9

babel-1.6_3
Converts among various molecular file formats
Long description | Sources | Main Web Site
Maintained by: [email protected]
Also listed in: Converters

belvu-2.29
A viewer for multiple sequence alignments
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: linux_base-f10-10_5

biococoa-1.6.0_2
Bioinformatics framework
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: aspell-0.60.6.1_2, cups-client-1.5.2_2, damageproto-1.2.1, dri2proto-2.6, expat-2.0.1_2, fixesproto-5.0, flac-1.2.1_3, fontconfig-2.9.0,1, freetype2-2.4.9_1, gettext-0.18.1.1, giflib-4.2.0_2, gmake-3.82_1, gmp-5.0.5, gnustep-back-0.22.0, gnustep-base-1.24.0, gnustep-gui-0.22.0, gnustep-make-2.6.2, gnutls-2.12.18_1, jbigkit-1.6, jpeg-8_3, kbproto-1.0.5, libGL-7.6.1_2, libGLU-7.6.1_1, libICE-1.0.7,1, libSM-1.2.0,1, libX11-1.4.4,1, libXau-1.0.6, libXdamage-1.1.3, libXdmcp-1.1.0, libXext-1.3.0_1,1, libXfixes-5.0, libXft-2.1.14, libXmu-1.1.0,1, libXrender-0.9.6, libXt-1.1.1,1, libXxf86vm-1.1.1, libao-1.1.0_1, libdrm-2.4.17_1, libffi-3.0.9, libgcrypt-1.5.0_1, libgpg-error-1.10, libiconv-1.14, libogg-1.3.0,4, libpciaccess-0.12.1, libpthread-stubs-0.3_3, libsndfile-1.0.25_2, libvorbis-1.3.3_1,3, libxcb-1.7, libxml2-2.7.8_5, libxslt-1.1.26_3, mDNSResponder-333.10, nettle-2.5, p11-kit-0.14, pciids-20120906, pkgconf-0.8.9, png-1.5.12, renderproto-0.11.1, tiff-4.0.2_1, xextproto-7.2.0, xf86vidmodeproto-2.3.1, xproto-7.0.22
Also listed in: Gnustep

biojava-1.7
Open-source Java tools for processing biological data
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: apache-ant-1.8.4, dejavu-2.33, expat-2.0.1_2, fontconfig-2.9.0,1, freetype2-2.4.9_1, inputproto-2.0.2, java-zoneinfo-2012.h, javavmwrapper-2.4_2, jpeg-8_3, kbproto-1.0.5, libICE-1.0.7,1, libSM-1.2.0,1, libX11-1.4.4,1, libXau-1.0.6, libXaw-1.0.9,2, libXdmcp-1.1.0, libXext-1.3.0_1,1, libXft-2.1.14, libXi-1.4.5,1, libXmu-1.1.0,1, libXp-1.0.1,1, libXpm-3.5.9, libXrender-0.9.6, libXt-1.1.1,1, libXtst-1.2.0, libiconv-1.14, libpthread-stubs-0.3_3, libxcb-1.7, open-motif-2.3.4, openjdk6-b27, pkgconf-0.8.9, png-1.5.12, printproto-1.0.5, recordproto-1.14.1, renderproto-0.11.1, xbitmaps-1.1.1, xextproto-7.2.0, xproto-7.0.22
Also listed in: Java

blat-34
A fast tool for local sequence similarity searches
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: gettext-0.18.1.1, gmake-3.82_1, libiconv-1.14

boinc-simap-5.10.5.09_4
Similarity Matrix of Proteins project for BOINC
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: ORBit2-2.14.19, atk-2.0.1, bitstream-vera-1.10_5, boinc-client-7.0.28_2, ca_root_nss-3.14, cairo-1.10.2_4,2, compat6x-i386-6.4.604000.200810_3, compositeproto-0.4.2, cups-client-1.5.2_2, curl-7.24.0_1, damageproto-1.2.1, dbus-1.4.14_4, dbus-glib-0.94, dconf-0.5.1_4, dri2proto-2.6, eggdbus-0.6_1, encodings-1.0.4,1, expat-2.0.1_2, fixesproto-5.0, font-bh-ttf-1.0.3, font-misc-ethiopic-1.0.3, font-misc-meltho-1.0.3, font-util-1.2.0, fontconfig-2.9.0,1, freeglut-2.8.0, freetype2-2.4.9_1, gamin-0.1.10_4, gconf2-2.32.0_3, gdk-pixbuf-2.23.5_3, gettext-0.18.1.1, gio-fam-backend-2.28.8_1, glib-2.28.8_4, gnome_subr-1.0, gnomehier-2.3_12, gobject-introspection-0.10.8_2, gstreamer-0.10.36, gstreamer-plugins-0.10.36_2,3, gtk-2.24.6_2, gtk-update-icon-cache-2.24.6_1, hicolor-icon-theme-0.12, inputproto-2.0.2, jasper-1.900.1_10, jbigkit-1.6, jpeg-8_3, kbproto-1.0.5, libGL-7.6.1_2, libGLU-7.6.1_1, libICE-1.0.7,1, libIDL-0.8.14_1, libSM-1.2.0,1, libX11-1.4.4,1, libXau-1.0.6, libXcomposite-0.4.3,1, libXcursor-1.1.12, libXdamage-1.1.3, libXdmcp-1.1.0, libXext-1.3.0_1,1, libXfixes-5.0, libXft-2.1.14, libXi-1.4.5,1, libXinerama-1.1.1,1, libXmu-1.1.0,1, libXrandr-1.3.2, libXrender-0.9.6, libXt-1.1.1,1, libXv-1.0.6,1, libXxf86vm-1.1.1, libdrm-2.4.17_1, libffi-3.0.9, libfontenc-1.1.0, libgee-0.6.2.1, libiconv-1.14, libmspack-0.3, libnotify-0.7.3_2, libpciaccess-0.12.1, libpthread-stubs-0.3_3, libxcb-1.7, libxml2-2.7.8_5, mkfontdir-1.0.6, mkfontscale-1.0.9, orc-0.4.16, pango-1.28.4_1, pciids-20120906, pcre-8.31_1, perl-5.14.2_2, pixman-0.24.2, pkgconf-0.8.9, png-1.5.12, polkit-0.99, python27-2.7.3_3, randrproto-1.3.2, renderproto-0.11.1, shared-mime-info-1.0_1, sqlite3-3.7.14.1, tiff-4.0.2_1, videoproto-2.3.1, wxgtk2-2.8.12_1, wxgtk2-common-2.8.12_1, xcb-util-0.3.8,1, xcb-util-renderutil-0.3.8, xextproto-7.2.0, xf86vidmodeproto-2.3.1, xineramaproto-1.2.1, xorg-fonts-truetype-7.5.1, xproto-7.0.22

chemeq-1.50_1
Outputs LaTeX code for chemical reaction
Long description | Sources
Maintained by: [email protected]
Requires: bison-2.5.1,1, gettext-0.18.1.1, libiconv-1.14, m4-1.4.16_1,1
Also listed in: Textproc

clustalw-2.1_1
A multiple alignment program for DNA or proteins
Long description | Sources | Main Web Site
Maintained by: [email protected]

consed-16.0
A graphical tool for editing Phrap assemblies
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: linux-f10-expat-2.0.1, linux-f10-fontconfig-2.6.0, linux-f10-xorg-libs-7.4_1, linux_base-f10-10_5, perl-5.14.2_2, phd2fasta-0.990622.f, phrap-0.990329, phred-0.020425.c

crux-1.2.0_1
Software toolkit for phylogenetic inference
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: binutils-2.22_3, gcc-4.6.3, gettext-0.18.1.1, gmake-3.82_1, gmp-5.0.5, libiconv-1.14, mpc-0.9, mpfr-3.1.1, python27-2.7.3_3
Also listed in: Python

cycle-0.3.1_5
A calendar program for women
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: ORBit2-2.14.19, atk-2.0.1, binutils-2.22_3, bitstream-vera-1.10_5, blas-3.4.1, cairo-1.10.2_4,2, compositeproto-0.4.2, cups-client-1.5.2_2, damageproto-1.2.1, dbus-1.4.14_4, dbus-glib-0.94, dconf-0.5.1_4, dri2proto-2.6, eggdbus-0.6_1, encodings-1.0.4,1, expat-2.0.1_2, fixesproto-5.0, font-bh-ttf-1.0.3, font-misc-ethiopic-1.0.3, font-misc-meltho-1.0.3, font-util-1.2.0, fontconfig-2.9.0,1, freeglut-2.8.0, freetype2-2.4.9_1, gamin-0.1.10_4, gcc-4.6.3, gconf2-2.32.0_3, gdk-pixbuf-2.23.5_3, gettext-0.18.1.1, gio-fam-backend-2.28.8_1, glib-2.28.8_4, gmp-5.0.5, gnome_subr-1.0, gnomehier-2.3_12, gobject-introspection-0.10.8_2, gstreamer-0.10.36, gstreamer-plugins-0.10.36_2,3, gtk-2.24.6_2, gtk-update-icon-cache-2.24.6_1, hicolor-icon-theme-0.12, inputproto-2.0.2, jasper-1.900.1_10, jbigkit-1.6, jpeg-8_3, kbproto-1.0.5, lapack-3.4.1, lcms-1.19_1,1, libGL-7.6.1_2, libGLU-7.6.1_1, libICE-1.0.7,1, libIDL-0.8.14_1, libSM-1.2.0,1, libX11-1.4.4,1, libXau-1.0.6, libXcomposite-0.4.3,1, libXcursor-1.1.12, libXdamage-1.1.3, libXdmcp-1.1.0, libXext-1.3.0_1,1, libXfixes-5.0, libXft-2.1.14, libXi-1.4.5,1, libXinerama-1.1.1,1, libXrandr-1.3.2, libXrender-0.9.6, libXt-1.1.1,1, libXv-1.0.6,1, libXxf86vm-1.1.1, libdrm-2.4.17_1, libffi-3.0.9, libfontenc-1.1.0, libgee-0.6.2.1, libiconv-1.14, libmspack-0.3, libpciaccess-0.12.1, libpthread-stubs-0.3_3, libxcb-1.7, libxml2-2.7.8_5, mkfontdir-1.0.6, mkfontscale-1.0.9, mpc-0.9, mpfr-3.1.1, orc-0.4.16, pango-1.28.4_1, pciids-20120906, pcre-8.31_1, perl-5.14.2_2, pixman-0.24.2, pkgconf-0.8.9, png-1.5.12, polkit-0.99, py27-imaging-1.1.7_1, py27-nose-1.2.1, py27-numpy-1.6.2_1,1, py27-opengl-3.0.1_1, py27-setuptools-0.6c11_3, py27-tkinter-2.7.3_3, py27-wxPython-2.8.12.1_1, py27-wxPython-common-2.8.12.1_1, python27-2.7.3_3, randrproto-1.3.2, renderproto-0.11.1, shared-mime-info-1.0_1, suitesparse-3.6.1_2, tcl-8.5.12_2, tcl-modules-8.5.12_2, tiff-4.0.2_1, tk-8.5.12, videoproto-2.3.1, wxgtk2-2.8.12_1, wxgtk2-common-2.8.12_1, wxgtk2-contrib-2.8.12_1, wxgtk2-contrib-common-2.8.12_1, xcb-util-0.3.8,1, xcb-util-renderutil-0.3.8, xextproto-7.2.0, xf86vidmodeproto-2.3.1, xineramaproto-1.2.1, xorg-fonts-truetype-7.5.1, xproto-7.0.22
Also listed in: Deskutils, Python

dotter-20021204
A viewer for multiple sequence alignments
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: linux_base-f10-10_5

dtiquery-1.1_5
Stanford DTI Visualization tool
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: ORBit2-2.14.19, atk-2.0.1, bitstream-vera-1.10_5, ca_root_nss-3.14, cairo-1.10.2_4,2, compositeproto-0.4.2, cups-client-1.5.2_2, damageproto-1.2.1, dbus-1.4.14_4, dbus-glib-0.94, dconf-0.5.1_4, dri2proto-2.6, eggdbus-0.6_1, encodings-1.0.4,1, expat-2.0.1_2, fixesproto-5.0, font-bh-ttf-1.0.3, font-misc-ethiopic-1.0.3, font-misc-meltho-1.0.3, font-util-1.2.0, fontconfig-2.9.0,1, freetype2-2.4.9_1, gamin-0.1.10_4, gconf2-2.32.0_3, gdk-pixbuf-2.23.5_3, gettext-0.18.1.1, gio-fam-backend-2.28.8_1, gl2ps-1.3.7, glib-2.28.8_4, gmake-3.82_1, gnome_subr-1.0, gnomehier-2.3_12, gobject-introspection-0.10.8_2, gstreamer-0.10.36, gstreamer-plugins-0.10.36_2,3, gtk-2.24.6_2, gtk-update-icon-cache-2.24.6_1, hicolor-icon-theme-0.12, inputproto-2.0.2, jama-1.2.5, jasper-1.900.1_10, jbigkit-1.6, jpeg-8_3, kbproto-1.0.5, kdehier4-1.0.10, libGL-7.6.1_2, libGLU-7.6.1_1, libICE-1.0.7,1, libIDL-0.8.14_1, libSM-1.2.0,1, libX11-1.4.4,1, libXau-1.0.6, libXcomposite-0.4.3,1, libXcursor-1.1.12, libXdamage-1.1.3, libXdmcp-1.1.0, libXext-1.3.0_1,1, libXfixes-5.0, libXft-2.1.14, libXi-1.4.5,1, libXinerama-1.1.1,1, libXmu-1.1.0,1, libXrandr-1.3.2, libXrender-0.9.6, libXt-1.1.1,1, libXv-1.0.6,1, libXxf86vm-1.1.1, libdrm-2.4.17_1, libffi-3.0.9, libfontenc-1.1.0, libgee-0.6.2.1, libiconv-1.14, libmspack-0.3, libpciaccess-0.12.1, libpthread-stubs-0.3_3, libxcb-1.7, libxml2-2.7.8_5, mkfontdir-1.0.6, mkfontscale-1.0.9, orc-0.4.16, pango-1.28.4_1, pciids-20120906, pcre-8.31_1, perl-5.14.2_2, phonon-4.6.0_1, pixman-0.24.2, pkgconf-0.8.9, png-1.5.12, polkit-0.99, python27-2.7.3_3, qt4-assistant-4.8.2, qt4-clucene-4.8.2, qt4-corelib-4.8.2, qt4-dbus-4.8.2, qt4-declarative-4.8.2, qt4-designer-4.8.2, qt4-doc-4.8.2, qt4-gui-4.8.2_1, qt4-help-4.8.2, qt4-network-4.8.2, qt4-opengl-4.8.2, qt4-qt3support-4.8.2, qt4-qtestlib-4.8.2, qt4-script-4.8.2, qt4-sql-4.8.2, qt4-sqlite-plugin-4.8.2, qt4-svg-4.8.2, qt4-webkit-4.8.2, qt4-xml-4.8.2, qt4-xmlpatterns-4.8.2, qzeitgeist-0.8.0, randrproto-1.3.2, rapid-2.01, renderproto-0.11.1, shared-mime-info-1.0_1, sqlite3-3.7.14.1, tcl-8.5.12_2, tcl-modules-8.5.12_2, tiff-4.0.2_1, tk-8.5.12, tnt-1.2.6, videoproto-2.3.1, vtk-5.10.1, wxgtk2-2.8.12_1, wxgtk2-common-2.8.12_1, xcb-util-0.3.8,1, xcb-util-renderutil-0.3.8, xdg-utils-1.0.2_7, xextproto-7.2.0, xf86vidmodeproto-2.3.1, xineramaproto-1.2.1, xorg-fonts-truetype-7.5.1, xproto-7.0.22
Also listed in: Science

embassy-6.2.0_2
A collection of contributed EMBOSS applications
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: emboss-6.2.0_2, expat-2.0.1_2, fontconfig-2.9.0,1, freetype2-2.4.9_1, gd-2.0.35_8,1, gettext-0.18.1.1, gmake-3.82_1, jpeg-8_3, kbproto-1.0.5, libICE-1.0.7,1, libSM-1.2.0,1, libX11-1.4.4,1, libXau-1.0.6, libXaw-1.0.9,2, libXdmcp-1.1.0, libXext-1.3.0_1,1, libXft-2.1.14, libXmu-1.1.0,1, libXp-1.0.1,1, libXpm-3.5.9, libXrender-0.9.6, libXt-1.1.1,1, libiconv-1.14, libpthread-stubs-0.3_3, libxcb-1.7, open-motif-2.3.4, pkgconf-0.8.9, png-1.5.12, printproto-1.0.5, renderproto-0.11.1, xbitmaps-1.1.1, xextproto-7.2.0, xproto-7.0.22

emboss-6.2.0_2
A collection of open source tools for genetic sequence analysis
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: clustalw-2.1_1, expat-2.0.1_2, fontconfig-2.9.0,1, freetype2-2.4.9_1, gd-2.0.35_8,1, gettext-0.18.1.1, gmake-3.82_1, jpeg-8_3, kbproto-1.0.5, libICE-1.0.7,1, libSM-1.2.0,1, libX11-1.4.4,1, libXau-1.0.6, libXaw-1.0.9,2, libXdmcp-1.1.0, libXext-1.3.0_1,1, libXft-2.1.14, libXmu-1.1.0,1, libXp-1.0.1,1, libXpm-3.5.9, libXrender-0.9.6, libXt-1.1.1,1, libiconv-1.14, libpthread-stubs-0.3_3, libtool-2.4.2, libxcb-1.7, open-motif-2.3.4, pkgconf-0.8.9, png-1.5.12, primer3-1.1.4, printproto-1.0.5, renderproto-0.11.1, xbitmaps-1.1.1, xextproto-7.2.0, xproto-7.0.22

fasta-21.1.1
A collection of programs for searching DNA and protein databases
Long description | Sources | Main Web Site
Maintained by: [email protected]

fasta3-36.3.2
A collection of programs for searching DNA and protein databases
Long description | Sources | Main Web Site
Maintained by: [email protected]

fastdnaml-1.2.2_2
Faster DNAML, makes phylogenetic trees using maximum likelihood
Long description | Sources | Main Web Site
Maintained by: [email protected]

finchtv-1.3.1
A chromatogram trace viewer
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: linux_base-f10-10_5

fluctuate-1.40
A program to fit population models
Long description | Sources | Main Web Site
Maintained by: [email protected]

garlic-1.6
Molecular viewer, editor, and visualization program
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: gettext-0.18.1.1, gmake-3.82_1, kbproto-1.0.5, libX11-1.4.4,1, libXau-1.0.6, libXdmcp-1.1.0, libiconv-1.14, libpthread-stubs-0.3_3, libxcb-1.7, pkgconf-0.8.9, xproto-7.0.22

genpak-0.26_8
A set of small utilities to manipulate DNA sequences
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: expat-2.0.1_2, fontconfig-2.9.0,1, freetype2-2.4.9_1, gd-2.0.35_8,1, gettext-0.18.1.1, gmake-3.82_1, jpeg-8_3, libiconv-1.14, pkgconf-0.8.9, png-1.5.12

gff2ps-0.98d_2
Converts gff-formated genomic data-sets to PostScript
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: bash-4.2.37, gawk-4.0.1, gettext-0.18.1.1, libiconv-1.14, libsigsegv-2.10

gmap-2006.04.21
A Genomic Mapping and Alignment Program for mRNA and EST Sequences
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: gettext-0.18.1.1, gmake-3.82_1, libiconv-1.14

gperiodic-2.0.10_7
Displays a periodic table of the elements
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: atk-2.0.1, bitstream-vera-1.10_5, cairo-1.10.2_4,2, compositeproto-0.4.2, cups-client-1.5.2_2, damageproto-1.2.1, encodings-1.0.4,1, expat-2.0.1_2, fixesproto-5.0, font-bh-ttf-1.0.3, font-misc-ethiopic-1.0.3, font-misc-meltho-1.0.3, font-util-1.2.0, fontconfig-2.9.0,1, freetype2-2.4.9_1, gamin-0.1.10_4, gdk-pixbuf-2.23.5_3, gettext-0.18.1.1, gio-fam-backend-2.28.8_1, glib-2.28.8_4, gobject-introspection-0.10.8_2, gtk-2.24.6_2, gtk-update-icon-cache-2.24.6_1, hicolor-icon-theme-0.12, inputproto-2.0.2, intltool-0.41.1, jasper-1.900.1_10, jbigkit-1.6, jpeg-8_3, kbproto-1.0.5, libICE-1.0.7,1, libSM-1.2.0,1, libX11-1.4.4,1, libXau-1.0.6, libXcomposite-0.4.3,1, libXcursor-1.1.12, libXdamage-1.1.3, libXdmcp-1.1.0, libXext-1.3.0_1,1, libXfixes-5.0, libXft-2.1.14, libXi-1.4.5,1, libXinerama-1.1.1,1, libXrandr-1.3.2, libXrender-0.9.6, libXt-1.1.1,1, libffi-3.0.9, libfontenc-1.1.0, libiconv-1.14, libpthread-stubs-0.3_3, libxcb-1.7, libxml2-2.7.8_5, mkfontdir-1.0.6, mkfontscale-1.0.9, p5-XML-Parser-2.41, pango-1.28.4_1, pcre-8.31_1, perl-5.14.2_2, pixman-0.24.2, pkgconf-0.8.9, png-1.5.12, python27-2.7.3_3, randrproto-1.3.2, renderproto-0.11.1, shared-mime-info-1.0_1, tiff-4.0.2_1, xcb-util-0.3.8,1, xcb-util-renderutil-0.3.8, xextproto-7.2.0, xineramaproto-1.2.1, xorg-fonts-truetype-7.5.1, xproto-7.0.22

grappa-2.0
Genome Rearrangements Analysis and Phylogeny Software
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: gettext-0.18.1.1, gmake-3.82_1, libiconv-1.14

hmmer-2.3.2
Profile hidden Markov models for biological sequence analysis
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: perl-5.14.2_2

io_lib-1.12.5
A general purpose trace file(and Experiment File) reading interface
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: ca_root_nss-3.14, curl-7.24.0_1, gettext-0.18.1.1, gmake-3.82_1, libiconv-1.14, libtool-2.4.2

jalview-2.07_2
A viewer and editor for multiple sequence alignments
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: apache-ant-1.8.4, dejavu-2.33, expat-2.0.1_2, fontconfig-2.9.0,1, freetype2-2.4.9_1, inputproto-2.0.2, java-zoneinfo-2012.h, javavmwrapper-2.4_2, jpeg-8_3, kbproto-1.0.5, libICE-1.0.7,1, libSM-1.2.0,1, libX11-1.4.4,1, libXau-1.0.6, libXaw-1.0.9,2, libXdmcp-1.1.0, libXext-1.3.0_1,1, libXft-2.1.14, libXi-1.4.5,1, libXmu-1.1.0,1, libXp-1.0.1,1, libXpm-3.5.9, libXrender-0.9.6, libXt-1.1.1,1, libXtst-1.2.0, libiconv-1.14, libpthread-stubs-0.3_3, libxcb-1.7, open-motif-2.3.4, openjdk6-b27, pkgconf-0.8.9, png-1.5.12, printproto-1.0.5, recordproto-1.14.1, renderproto-0.11.1, xbitmaps-1.1.1, xextproto-7.2.0, xproto-7.0.22
Also listed in: Java

lagan-1.2
Efficient tools for large-scale multiple alignments of genomic DNA
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: perl-5.14.2_2

lamarc-2.1.8
A package of programs for computing population parameters
Long description | Sources | Main Web Site
Maintained by: [email protected]

libgenome-0.5.2_1
Toolkit for developing bioinformatic related software in C++
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: libtool-2.4.2

libsbml-4.2.0
An API Library for Working with SBML File
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: gettext-0.18.1.1, gmake-3.82_1, libiconv-1.14, libxml2-2.7.8_5, pkgconf-0.8.9
Also listed in: Devel

linux-foldingathome-5.04
Distributed client for Protein Folding
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: linux_base-f10-10_5

mafft-6.903
Multiple alignment program for amino acid or nucleotide sequences
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: fasta3-36.3.2, gettext-0.18.1.1, gmake-3.82_1, libiconv-1.14

mapm3-3.0
Constructs linkage maps of markers segregating in experimental crosses
Long description | Sources | Main Web Site
Maintained by: [email protected]

migrate-3.1.6
A program to estimate population sizes and migration rates
Long description | Sources | Main Web Site
Maintained by: [email protected]

minc-1.5.1
Medical Imaging NetCDF
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: libtool-2.4.2, netcdf-3.6.3_4
Also listed in: Science

minc-2.0.18
Medical Imaging NetCDF
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: hdf5-1.6.9_1, libtool-2.4.2, netcdf-3.6.3_4
Also listed in: Science

molden-4.6_3
Display molecular orbitals and electron densities in 2D and 3D
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: binutils-2.22_3, damageproto-1.2.1, dri2proto-2.6, expat-2.0.1_2, fixesproto-5.0, freeglut-2.8.0, gcc-4.6.3, gettext-0.18.1.1, gmp-5.0.5, inputproto-2.0.2, kbproto-1.0.5, libGL-7.6.1_2, libGLU-7.6.1_1, libICE-1.0.7,1, libSM-1.2.0,1, libX11-1.4.4,1, libXau-1.0.6, libXdamage-1.1.3, libXdmcp-1.1.0, libXext-1.3.0_1,1, libXfixes-5.0, libXi-1.4.5,1, libXmu-1.1.0,1, libXrandr-1.3.2, libXrender-0.9.6, libXt-1.1.1,1, libXxf86vm-1.1.1, libdrm-2.4.17_1, libiconv-1.14, libpciaccess-0.12.1, libpthread-stubs-0.3_3, libxcb-1.7, mpc-0.9, mpfr-3.1.1, pciids-20120906, pkgconf-0.8.9, randrproto-1.3.2, renderproto-0.11.1, xextproto-7.2.0, xf86vidmodeproto-2.3.1, xproto-7.0.22

mopac-7.1.11_1
Semi-empirical (MNDO, etc.) molecular orbital calculation
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: autoconf-2.69, autoconf-wrapper-20101119, automake-1.12.4, automake-wrapper-20101119, f2c-20060810_3, gettext-0.18.1.1, gmake-3.82_1, libiconv-1.14, libtool-2.4.2, m4-1.4.16_1,1, perl-5.14.2_2

mrbayes-3.1.2_1
Bayesian inference of phylogeny
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: gettext-0.18.1.1, gmake-3.82_1, libiconv-1.14, readline-6.2_1

mummer-3.23
A modular system for rapid whole genome alignment
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: gettext-0.18.1.1, gmake-3.82_1, libiconv-1.14

muscle-3.6
Multiple Sequence Comparison by Log-Expectation
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: gettext-0.18.1.1, gmake-3.82_1, libiconv-1.14

ncbi-toolkit-2009.03.01_1
NCBI development toolkit, including BLAST 2 and GenBank/Entrez support
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: expat-2.0.1_2, fontconfig-2.9.0,1, freetype2-2.4.9_1, jpeg-8_3, kbproto-1.0.5, libICE-1.0.7,1, libSM-1.2.0,1, libX11-1.4.4,1, libXau-1.0.6, libXaw-1.0.9,2, libXdmcp-1.1.0, libXext-1.3.0_1,1, libXft-2.1.14, libXmu-1.1.0,1, libXp-1.0.1,1, libXpm-3.5.9, libXrender-0.9.6, libXt-1.1.1,1, libiconv-1.14, libpthread-stubs-0.3_3, libxcb-1.7, open-motif-2.3.4, pkgconf-0.8.9, png-1.5.12, printproto-1.0.5, renderproto-0.11.1, xbitmaps-1.1.1, xextproto-7.2.0, xproto-7.0.22

njplot-2.1_2
Phylogenetic tree drawing program capable of interactive manipulation
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: expat-2.0.1_2, fontconfig-2.9.0,1, freetype2-2.4.9_1, jpeg-8_3, kbproto-1.0.5, libICE-1.0.7,1, libSM-1.2.0,1, libX11-1.4.4,1, libXau-1.0.6, libXaw-1.0.9,2, libXdmcp-1.1.0, libXext-1.3.0_1,1, libXft-2.1.14, libXmu-1.1.0,1, libXp-1.0.1,1, libXpm-3.5.9, libXrender-0.9.6, libXt-1.1.1,1, libiconv-1.14, libpthread-stubs-0.3_3, libxcb-1.7, ncbi-toolkit-2009.03.01_1, open-motif-2.3.4, pkgconf-0.8.9, png-1.5.12, printproto-1.0.5, renderproto-0.11.1, xbitmaps-1.1.1, xextproto-7.2.0, xproto-7.0.22

ortep3-1.0.3_5
The Oak Ridge Thermal Ellipsoid Plot Program for Crystal Structure
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: binutils-2.22_3, gcc-4.6.3, gettext-0.18.1.1, gmp-5.0.5, libiconv-1.14, mpc-0.9, mpfr-3.1.1

p5-AcePerl-1.92_2
Perl5 interface to the ACEDB genome database system
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: p5-Cache-2.04_1, p5-Cache-Cache-1.06, p5-Digest-SHA1-2.13, p5-Error-0.17018, p5-File-NFSLock-1.21, p5-Heap-0.80, p5-IO-String-1.08, p5-IPC-ShareLite-0.17, p5-TimeDate-1.20,1, perl-5.14.2_2
Also listed in: Databases, Perl5

p5-Bio-ASN1-EntrezGene-1.091
Regular expression-based Perl Parser for NCBI Entrez Gene
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: perl-5.14.2_2
Also listed in: Perl5

p5-Bio-Das-1.17_2
Client-side library for Distributed Genome Annotation System
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: bitstream-vera-1.10_5, cairo-1.10.2_4,2, encodings-1.0.4,1, expat-2.0.1_2, font-bh-ttf-1.0.3, font-misc-ethiopic-1.0.3, font-misc-meltho-1.0.3, font-util-1.2.0, fontconfig-2.9.0,1, freetype2-2.4.9_1, gamin-0.1.10_4, gd-2.0.35_8,1, gettext-0.18.1.1, gio-fam-backend-2.28.8_1, glib-2.28.8_4, gobject-introspection-0.10.8_2, graphviz-2.28.0_1, jpeg-8_3, kbproto-1.0.5, libICE-1.0.7,1, libSM-1.2.0,1, libX11-1.4.4,1, libXau-1.0.6, libXaw-1.0.9,2, libXdmcp-1.1.0, libXext-1.3.0_1,1, libXft-2.1.14, libXmu-1.1.0,1, libXp-1.0.1,1, libXpm-3.5.9, libXrender-0.9.6, libXt-1.1.1,1, libffi-3.0.9, libfontenc-1.1.0, libiconv-1.14, libltdl-2.4.2, libpthread-stubs-0.3_3, libxcb-1.7, mkfontdir-1.0.6, mkfontscale-1.0.9, mysql-client-5.5.28, p5-AcePerl-1.92_2, p5-Algorithm-C3-0.08, p5-Algorithm-Munkres-0.08, p5-Array-Compare-2.02, p5-Authen-NTLM-1.09, p5-Bio-ASN1-EntrezGene-1.091, p5-Cache-2.04_1, p5-Cache-Cache-1.06, p5-Class-AutoClass-1.01, p5-Class-C3-0.24, p5-Class-Inspector-1.27, p5-Class-Load-0.20, p5-Class-Load-XS-0.05, p5-Clone-0.31, p5-Convert-BinHex-1.119, p5-Convert-Binary-C-0.76, p5-Crypt-RC4-2.02, p5-Crypt-SSLeay-0.64, p5-DBD-mysql-4.021, p5-DBI-1.622, p5-Data-OptList-0.107, p5-Data-Stag-0.11, p5-Devel-GlobalDestruction-0.09, p5-Digest-HMAC-1.03, p5-Digest-Perl-MD5-1.8, p5-Digest-SHA1-2.13, p5-Dist-CheckConflicts-0.02, p5-Email-Date-Format-1.002, p5-Encode-Locale-1.03, p5-Error-0.17018, p5-Eval-Closure-0.08, p5-File-Listing-6.04, p5-File-NFSLock-1.21, p5-GD-2.46_1, p5-GD-SVG-0.33_4, p5-Graph-0.94,1, p5-GraphViz-2.10_1, p5-HTML-Parser-3.69, p5-HTML-Tagset-3.20, p5-HTML-Tree-4.2, p5-HTTP-Cookies-6.01, p5-HTTP-Daemon-6.01, p5-HTTP-Date-6.02, p5-HTTP-Message-6.06, p5-HTTP-Negotiate-6.01, p5-Heap-0.80, p5-IO-Socket-IP-0.17, p5-IO-Socket-SSL-1.76, p5-IO-String-1.08, p5-IO-Tty-1.10, p5-IO-stringy-2.110, p5-IPC-Run-0.92, p5-IPC-ShareLite-0.17, p5-LWP-MediaTypes-6.02, p5-LWP-Protocol-https-6.03, p5-List-MoreUtils-0.33, p5-MIME-Lite-3.02.9, p5-MIME-Tools-5.503,2, p5-MIME-Types-1.35, p5-MRO-Compat-0.11, p5-Mail-Tools-2.11, p5-Math-Derivative-0.01, p5-Math-Random-0.71, p5-Math-Spline-0.01, p5-Module-Implementation-0.06, p5-Module-Runtime-0.013, p5-Moose-2.0604, p5-Mozilla-CA-20120823_1, p5-Net-HTTP-6.03_1, p5-Net-SSLeay-1.49, p5-OLE-Storage_Lite-0.19, p5-Package-DeprecationManager-0.13, p5-Package-Stash-0.33, p5-Package-Stash-XS-0.25, p5-Params-Util-1.07, p5-Parse-RecDescent-1.967.009_1, p5-PostScript-0.06, p5-SOAP-Lite-0.715, p5-SVG-2.53, p5-SVG-Graph-0.04, p5-Scalar-List-Utils-1.25,1, p5-Set-Scalar-1.25, p5-Socket-2.006, p5-Spreadsheet-ParseExcel-0.59,1, p5-Statistics-Descriptive-3.0604, p5-Sub-Exporter-0.984, p5-Sub-Exporter-Progressive-0.001.004, p5-Sub-Install-0.926, p5-Sub-Name-0.05, p5-Task-Weaken-1.04, p5-Text-Iconv-1.7, p5-Text-Shellwords-1.08, p5-Tie-IxHash-1.22, p5-TimeDate-1.20,1, p5-Tree-DAG_Node-1.06, p5-Try-Tiny-0.11, p5-URI-1.60, p5-WWW-RobotRules-6.02, p5-XML-DOM-1.44, p5-XML-DOM-XPath-0.14, p5-XML-Filter-BufferText-1.01, p5-XML-NamespaceSupport-1.11, p5-XML-Parser-2.41, p5-XML-RegExp-0.04, p5-XML-SAX-0.99, p5-XML-SAX-Base-1.08, p5-XML-SAX-Writer-0.53, p5-XML-Twig-3.41, p5-XML-Writer-0.615, p5-XML-XPath-1.13, p5-XML-XPathEngine-0.13, p5-bioperl-1.6.1_4, p5-libwww-6.04, p5-libxml-0.08, pango-1.28.4_1, pcre-8.31_1, perl-5.14.2_2, pixman-0.24.2, pkgconf-0.8.9, png-1.5.12, printproto-1.0.5, python27-2.7.3_3, renderproto-0.11.1, xcb-util-0.3.8,1, xcb-util-renderutil-0.3.8, xextproto-7.2.0, xorg-fonts-truetype-7.5.1, xproto-7.0.22
Also listed in: Perl5

p5-Bio-Das-Lite-2.11
Perl extension for the DAS (HTTP+XML) Protocol
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: ca_root_nss-3.14, curl-7.24.0_1, p5-Authen-NTLM-1.09, p5-Digest-HMAC-1.03, p5-Encode-Locale-1.03, p5-File-Listing-6.04, p5-HTML-Parser-3.69, p5-HTML-Tagset-3.20, p5-HTTP-Cookies-6.01, p5-HTTP-Daemon-6.01, p5-HTTP-Date-6.02, p5-HTTP-Message-6.06, p5-HTTP-Negotiate-6.01, p5-IO-Socket-IP-0.17, p5-IO-Socket-SSL-1.76, p5-LWP-MediaTypes-6.02, p5-Module-Build-0.4003, p5-Net-HTTP-6.03_1, p5-Net-SSLeay-1.49, p5-Readonly-1.03_2, p5-Socket-2.006, p5-URI-1.60, p5-WWW-Curl-4.15, p5-WWW-RobotRules-6.02, p5-libwww-6.04, perl-5.14.2_2
Also listed in: Perl5

p5-Bio-GFF3-1.4
Fast low-level functions for parsing and formatting GFF3
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: p5-List-MoreUtils-0.33, p5-URI-1.60, perl-5.14.2_2
Also listed in: Perl5

p5-Bio-Glite-0.10_1
An Perl Interface to G-language
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: p5-Authen-NTLM-1.09, p5-Digest-HMAC-1.03, p5-Encode-Locale-1.03, p5-File-Listing-6.04, p5-HTML-Parser-3.69, p5-HTML-Tagset-3.20, p5-HTTP-Cookies-6.01, p5-HTTP-Daemon-6.01, p5-HTTP-Date-6.02, p5-HTTP-Message-6.06, p5-HTTP-Negotiate-6.01, p5-IO-Socket-IP-0.17, p5-IO-Socket-SSL-1.76, p5-LWP-MediaTypes-6.02, p5-Net-HTTP-6.03_1, p5-Net-SSLeay-1.49, p5-Socket-2.006, p5-URI-1.60, p5-WWW-RobotRules-6.02, p5-libwww-6.04, perl-5.14.2_2
Also listed in: Perl5

p5-Bio-Graphics-2.29
Generate GD Images of Bio::Seq Objects
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: bitstream-vera-1.10_5, ca_root_nss-3.14, cairo-1.10.2_4,2, curl-7.24.0_1, encodings-1.0.4,1, expat-2.0.1_2, font-bh-ttf-1.0.3, font-misc-ethiopic-1.0.3, font-misc-meltho-1.0.3, font-util-1.2.0, fontconfig-2.9.0,1, freetype2-2.4.9_1, gamin-0.1.10_4, gd-2.0.35_8,1, gettext-0.18.1.1, gio-fam-backend-2.28.8_1, glib-2.28.8_4, gobject-introspection-0.10.8_2, graphviz-2.28.0_1, io_lib-1.12.5, jpeg-8_3, kbproto-1.0.5, libICE-1.0.7,1, libSM-1.2.0,1, libX11-1.4.4,1, libXau-1.0.6, libXaw-1.0.9,2, libXdmcp-1.1.0, libXext-1.3.0_1,1, libXft-2.1.14, libXmu-1.1.0,1, libXp-1.0.1,1, libXpm-3.5.9, libXrender-0.9.6, libXt-1.1.1,1, libffi-3.0.9, libfontenc-1.1.0, libiconv-1.14, libltdl-2.4.2, libpthread-stubs-0.3_3, libxcb-1.7, mkfontdir-1.0.6, mkfontscale-1.0.9, mysql-client-5.5.28, p5-AcePerl-1.92_2, p5-Algorithm-C3-0.08, p5-Algorithm-Munkres-0.08, p5-Array-Compare-2.02, p5-Authen-NTLM-1.09, p5-Bio-ASN1-EntrezGene-1.091, p5-Bio-SCF-1.03, p5-Cache-2.04_1, p5-Cache-Cache-1.06, p5-Class-AutoClass-1.01, p5-Class-C3-0.24, p5-Class-Inspector-1.27, p5-Class-Load-0.20, p5-Class-Load-XS-0.05, p5-Clone-0.31, p5-Convert-BinHex-1.119, p5-Convert-Binary-C-0.76, p5-Crypt-RC4-2.02, p5-Crypt-SSLeay-0.64, p5-DBD-mysql-4.021, p5-DBI-1.622, p5-Data-OptList-0.107, p5-Data-Stag-0.11, p5-Devel-GlobalDestruction-0.09, p5-Digest-HMAC-1.03, p5-Digest-Perl-MD5-1.8, p5-Digest-SHA1-2.13, p5-Dist-CheckConflicts-0.02, p5-Email-Date-Format-1.002, p5-Encode-Locale-1.03, p5-Error-0.17018, p5-Eval-Closure-0.08, p5-File-Listing-6.04, p5-File-NFSLock-1.21, p5-GD-2.46_1, p5-GD-SVG-0.33_4, p5-Graph-0.94,1, p5-GraphViz-2.10_1, p5-HTML-Parser-3.69, p5-HTML-Tagset-3.20, p5-HTML-Tree-4.2, p5-HTTP-Cookies-6.01, p5-HTTP-Daemon-6.01, p5-HTTP-Date-6.02, p5-HTTP-Message-6.06, p5-HTTP-Negotiate-6.01, p5-Heap-0.80, p5-IO-Socket-IP-0.17, p5-IO-Socket-SSL-1.76, p5-IO-String-1.08, p5-IO-Tty-1.10, p5-IO-stringy-2.110, p5-IPC-Run-0.92, p5-IPC-ShareLite-0.17, p5-LWP-MediaTypes-6.02, p5-LWP-Protocol-https-6.03, p5-List-MoreUtils-0.33, p5-MIME-Lite-3.02.9, p5-MIME-Tools-5.503,2, p5-MIME-Types-1.35, p5-MRO-Compat-0.11, p5-Mail-Tools-2.11, p5-Math-Derivative-0.01, p5-Math-Random-0.71, p5-Math-Spline-0.01, p5-Module-Implementation-0.06, p5-Module-Runtime-0.013, p5-Moose-2.0604, p5-Mozilla-CA-20120823_1, p5-Net-HTTP-6.03_1, p5-Net-SSLeay-1.49, p5-OLE-Storage_Lite-0.19, p5-Package-DeprecationManager-0.13, p5-Package-Stash-0.33, p5-Package-Stash-XS-0.25, p5-Params-Util-1.07, p5-Parse-RecDescent-1.967.009_1, p5-PostScript-0.06, p5-SOAP-Lite-0.715, p5-SVG-2.53, p5-SVG-Graph-0.04, p5-Scalar-List-Utils-1.25,1, p5-Set-Scalar-1.25, p5-Socket-2.006, p5-Spreadsheet-ParseExcel-0.59,1, p5-Statistics-Descriptive-3.0604, p5-Sub-Exporter-0.984, p5-Sub-Exporter-Progressive-0.001.004, p5-Sub-Install-0.926, p5-Sub-Name-0.05, p5-Task-Weaken-1.04, p5-Text-Iconv-1.7, p5-Text-Shellwords-1.08, p5-Tie-IxHash-1.22, p5-TimeDate-1.20,1, p5-Tree-DAG_Node-1.06, p5-Try-Tiny-0.11, p5-URI-1.60, p5-WWW-RobotRules-6.02, p5-XML-DOM-1.44, p5-XML-DOM-XPath-0.14, p5-XML-Filter-BufferText-1.01, p5-XML-NamespaceSupport-1.11, p5-XML-Parser-2.41, p5-XML-RegExp-0.04, p5-XML-SAX-0.99, p5-XML-SAX-Base-1.08, p5-XML-SAX-Writer-0.53, p5-XML-Twig-3.41, p5-XML-Writer-0.615, p5-XML-XPath-1.13, p5-XML-XPathEngine-0.13, p5-bioperl-1.6.1_4, p5-libwww-6.04, p5-libxml-0.08, pango-1.28.4_1, pcre-8.31_1, perl-5.14.2_2, pixman-0.24.2, pkgconf-0.8.9, png-1.5.12, printproto-1.0.5, python27-2.7.3_3, renderproto-0.11.1, xcb-util-0.3.8,1, xcb-util-renderutil-0.3.8, xextproto-7.2.0, xorg-fonts-truetype-7.5.1, xproto-7.0.22
Also listed in: Perl5

p5-Bio-MAGETAB-1.26
A data model and utility API for the MAGE-TAB format
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: p5-Algorithm-C3-0.08, p5-B-Hooks-EndOfScope-0.11, p5-Carp-Clan-6.04, p5-Class-C3-0.24, p5-Class-Load-0.20, p5-Class-Load-XS-0.05, p5-Class-Singleton-1.4, p5-Data-OptList-0.107, p5-Date-Manip-6.34, p5-DateTime-0.77, p5-DateTime-Format-DateManip-0.04, p5-DateTime-Locale-0.45, p5-DateTime-TimeZone-1.50, p5-Devel-GlobalDestruction-0.09, p5-Digest-HMAC-1.03, p5-Dist-CheckConflicts-0.02, p5-Email-Valid-0.190, p5-Eval-Closure-0.08, p5-IO-Socket-INET6-2.69, p5-List-MoreUtils-0.33, p5-MRO-Compat-0.11, p5-Mail-Tools-2.11, p5-Math-Round-0.06, p5-Module-Implementation-0.06, p5-Module-Runtime-0.013, p5-Moose-2.0604, p5-MooseX-FollowPBP-0.05, p5-MooseX-Types-0.35, p5-Net-DNS-0.68, p5-Net-Domain-TLD-1.69, p5-Package-DeprecationManager-0.13, p5-Package-Stash-0.33, p5-Package-Stash-XS-0.25, p5-Params-Coerce-0.14_1, p5-Params-Util-1.07, p5-Params-Validate-1.06, p5-Parse-RecDescent-1.967.009_1, p5-Scalar-List-Utils-1.25,1, p5-Socket6-0.23, p5-Sub-Exporter-0.984, p5-Sub-Exporter-Progressive-0.001.004, p5-Sub-Identify-0.04, p5-Sub-Install-0.926, p5-Sub-Name-0.05, p5-Task-Weaken-1.04, p5-Text-CSV_XS-0.91, p5-TimeDate-1.20,1, p5-Try-Tiny-0.11, p5-URI-1.60, p5-Variable-Magic-0.51, p5-YAML-Syck-1.21, p5-namespace-clean-0.23, perl-5.14.2_2
Also listed in: Perl5

p5-Bio-NEXUS-0.78
An object-oriented Perl API for the NEXUS file format
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: p5-Clone-PP-1.02, perl-5.14.2_2
Also listed in: Perl5

p5-Bio-Phylo-0.50
Phylogenetic analysis using perl
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: bitstream-vera-1.10_5, cairo-1.10.2_4,2, encodings-1.0.4,1, expat-2.0.1_2, font-bh-ttf-1.0.3, font-misc-ethiopic-1.0.3, font-misc-meltho-1.0.3, font-util-1.2.0, fontconfig-2.9.0,1, freetype2-2.4.9_1, gamin-0.1.10_4, gd-2.0.35_8,1, gettext-0.18.1.1, gio-fam-backend-2.28.8_1, glib-2.28.8_4, gobject-introspection-0.10.8_2, graphviz-2.28.0_1, jpeg-8_3, kbproto-1.0.5, libICE-1.0.7,1, libSM-1.2.0,1, libX11-1.4.4,1, libXau-1.0.6, libXaw-1.0.9,2, libXdmcp-1.1.0, libXext-1.3.0_1,1, libXft-2.1.14, libXmu-1.1.0,1, libXp-1.0.1,1, libXpm-3.5.9, libXrender-0.9.6, libXt-1.1.1,1, libffi-3.0.9, libfontenc-1.1.0, libiconv-1.14, libltdl-2.4.2, libpthread-stubs-0.3_3, libxcb-1.7, libxml2-2.7.8_5, mkfontdir-1.0.6, mkfontscale-1.0.9, mysql-client-5.5.28, p5-AcePerl-1.92_2, p5-Algorithm-C3-0.08, p5-Algorithm-Munkres-0.08, p5-Array-Compare-2.02, p5-Authen-NTLM-1.09, p5-Bio-ASN1-EntrezGene-1.091, p5-Cache-2.04_1, p5-Cache-Cache-1.06, p5-Class-AutoClass-1.01, p5-Class-C3-0.24, p5-Class-Inspector-1.27, p5-Class-Load-0.20, p5-Class-Load-XS-0.05, p5-Clone-0.31, p5-Convert-BinHex-1.119, p5-Convert-Binary-C-0.76, p5-Crypt-RC4-2.02, p5-Crypt-SSLeay-0.64, p5-DBD-mysql-4.021, p5-DBI-1.622, p5-Data-OptList-0.107, p5-Data-Stag-0.11, p5-Data-TemporaryBag-0.09, p5-Devel-GlobalDestruction-0.09, p5-Digest-HMAC-1.03, p5-Digest-Perl-MD5-1.8, p5-Digest-SHA1-2.13, p5-Dist-CheckConflicts-0.02, p5-Email-Date-Format-1.002, p5-Encode-Locale-1.03, p5-Error-0.17018, p5-Eval-Closure-0.08, p5-File-Listing-6.04, p5-File-NFSLock-1.21, p5-Font-TTF-0.48, p5-GD-2.46_1, p5-GD-SVG-0.33_4, p5-Graph-0.94,1, p5-GraphViz-2.10_1, p5-HTML-Parser-3.69, p5-HTML-Tagset-3.20, p5-HTML-Tree-4.2, p5-HTTP-Cookies-6.01, p5-HTTP-Daemon-6.01, p5-HTTP-Date-6.02, p5-HTTP-Message-6.06, p5-HTTP-Negotiate-6.01, p5-Heap-0.80, p5-IO-Socket-IP-0.17, p5-IO-Socket-SSL-1.76, p5-IO-String-1.08, p5-IO-Tty-1.10, p5-IO-stringy-2.110, p5-IPC-Run-0.92, p5-IPC-ShareLite-0.17, p5-LWP-MediaTypes-6.02, p5-LWP-Protocol-https-6.03, p5-List-MoreUtils-0.33, p5-MIME-Lite-3.02.9, p5-MIME-Tools-5.503,2, p5-MIME-Types-1.35, p5-MRO-Compat-0.11, p5-Mail-Tools-2.11, p5-Math-Bezier-Convert-0.02, p5-Math-CDF-0.1, p5-Math-Derivative-0.01, p5-Math-Random-0.71, p5-Math-Spline-0.01, p5-Module-Implementation-0.06, p5-Module-Runtime-0.013, p5-Moose-2.0604, p5-Mozilla-CA-20120823_1, p5-Net-HTTP-6.03_1, p5-Net-SSLeay-1.49, p5-OLE-Storage_Lite-0.19, p5-PDF-API2-2.019, p5-Package-DeprecationManager-0.13, p5-Package-Stash-0.33, p5-Package-Stash-XS-0.25, p5-Params-Util-1.07, p5-Parse-RecDescent-1.967.009_1, p5-PostScript-0.06, p5-SOAP-Lite-0.715, p5-SVG-2.53, p5-SVG-Graph-0.04, p5-SWF-Builder-0.16, p5-SWF-File-0.42_1,1, p5-Scalar-List-Utils-1.25,1, p5-Set-Scalar-1.25, p5-Socket-2.006, p5-Spreadsheet-ParseExcel-0.59,1, p5-Statistics-Descriptive-3.0604, p5-Sub-Exporter-0.984, p5-Sub-Exporter-Progressive-0.001.004, p5-Sub-Install-0.926, p5-Sub-Name-0.05, p5-Task-Weaken-1.04, p5-Text-Iconv-1.7, p5-Text-Shellwords-1.08, p5-Tie-IxHash-1.22, p5-TimeDate-1.20,1, p5-Tree-DAG_Node-1.06, p5-Try-Tiny-0.11, p5-URI-1.60, p5-WWW-RobotRules-6.02, p5-XML-DOM-1.44, p5-XML-DOM-XPath-0.14, p5-XML-Filter-BufferText-1.01, p5-XML-LibXML-2.0004,1, p5-XML-NamespaceSupport-1.11, p5-XML-Parser-2.41, p5-XML-RegExp-0.04, p5-XML-SAX-0.99, p5-XML-SAX-Base-1.08, p5-XML-SAX-Writer-0.53, p5-XML-Twig-3.41, p5-XML-Writer-0.615, p5-XML-XML2JSON-0.06, p5-XML-XPath-1.13, p5-XML-XPathEngine-0.13, p5-YAML-Syck-1.21, p5-bioperl-1.6.1_4, p5-libwww-6.04, p5-libxml-0.08, pango-1.28.4_1, pcre-8.31_1, perl-5.14.2_2, pixman-0.24.2, pkgconf-0.8.9, png-1.5.12, printproto-1.0.5, python27-2.7.3_3, renderproto-0.11.1, xcb-util-0.3.8,1, xcb-util-renderutil-0.3.8, xextproto-7.2.0, xorg-fonts-truetype-7.5.1, xproto-7.0.22
Also listed in: Perl5

p5-Bio-SCF-1.03
Read and Update SCF Chromatographic Sequence Files
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: ca_root_nss-3.14, curl-7.24.0_1, io_lib-1.12.5, perl-5.14.2_2
Also listed in: Perl5

p5-bioperl-1.6.1_4
A collection of Perl modules for bioinformatics
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: bitstream-vera-1.10_5, cairo-1.10.2_4,2, encodings-1.0.4,1, expat-2.0.1_2, font-bh-ttf-1.0.3, font-misc-ethiopic-1.0.3, font-misc-meltho-1.0.3, font-util-1.2.0, fontconfig-2.9.0,1, freetype2-2.4.9_1, gamin-0.1.10_4, gd-2.0.35_8,1, gettext-0.18.1.1, gio-fam-backend-2.28.8_1, glib-2.28.8_4, gobject-introspection-0.10.8_2, graphviz-2.28.0_1, jpeg-8_3, kbproto-1.0.5, libICE-1.0.7,1, libSM-1.2.0,1, libX11-1.4.4,1, libXau-1.0.6, libXaw-1.0.9,2, libXdmcp-1.1.0, libXext-1.3.0_1,1, libXft-2.1.14, libXmu-1.1.0,1, libXp-1.0.1,1, libXpm-3.5.9, libXrender-0.9.6, libXt-1.1.1,1, libffi-3.0.9, libfontenc-1.1.0, libiconv-1.14, libltdl-2.4.2, libpthread-stubs-0.3_3, libxcb-1.7, mkfontdir-1.0.6, mkfontscale-1.0.9, mysql-client-5.5.28, p5-AcePerl-1.92_2, p5-Algorithm-C3-0.08, p5-Algorithm-Munkres-0.08, p5-Array-Compare-2.02, p5-Authen-NTLM-1.09, p5-Bio-ASN1-EntrezGene-1.091, p5-Cache-2.04_1, p5-Cache-Cache-1.06, p5-Class-AutoClass-1.01, p5-Class-C3-0.24, p5-Class-Inspector-1.27, p5-Class-Load-0.20, p5-Class-Load-XS-0.05, p5-Clone-0.31, p5-Convert-BinHex-1.119, p5-Convert-Binary-C-0.76, p5-Crypt-RC4-2.02, p5-Crypt-SSLeay-0.64, p5-DBD-mysql-4.021, p5-DBI-1.622, p5-Data-OptList-0.107, p5-Data-Stag-0.11, p5-Devel-GlobalDestruction-0.09, p5-Digest-HMAC-1.03, p5-Digest-Perl-MD5-1.8, p5-Digest-SHA1-2.13, p5-Dist-CheckConflicts-0.02, p5-Email-Date-Format-1.002, p5-Encode-Locale-1.03, p5-Error-0.17018, p5-Eval-Closure-0.08, p5-File-Listing-6.04, p5-File-NFSLock-1.21, p5-GD-2.46_1, p5-GD-SVG-0.33_4, p5-Graph-0.94,1, p5-GraphViz-2.10_1, p5-HTML-Parser-3.69, p5-HTML-Tagset-3.20, p5-HTML-Tree-4.2, p5-HTTP-Cookies-6.01, p5-HTTP-Daemon-6.01, p5-HTTP-Date-6.02, p5-HTTP-Message-6.06, p5-HTTP-Negotiate-6.01, p5-Heap-0.80, p5-IO-Socket-IP-0.17, p5-IO-Socket-SSL-1.76, p5-IO-String-1.08, p5-IO-Tty-1.10, p5-IO-stringy-2.110, p5-IPC-Run-0.92, p5-IPC-ShareLite-0.17, p5-LWP-MediaTypes-6.02, p5-LWP-Protocol-https-6.03, p5-List-MoreUtils-0.33, p5-MIME-Lite-3.02.9, p5-MIME-Tools-5.503,2, p5-MIME-Types-1.35, p5-MRO-Compat-0.11, p5-Mail-Tools-2.11, p5-Math-Derivative-0.01, p5-Math-Random-0.71, p5-Math-Spline-0.01, p5-Module-Build-0.4003, p5-Module-Implementation-0.06, p5-Module-Runtime-0.013, p5-Moose-2.0604, p5-Mozilla-CA-20120823_1, p5-Net-HTTP-6.03_1, p5-Net-SSLeay-1.49, p5-OLE-Storage_Lite-0.19, p5-Package-DeprecationManager-0.13, p5-Package-Stash-0.33, p5-Package-Stash-XS-0.25, p5-Params-Util-1.07, p5-Parse-RecDescent-1.967.009_1, p5-PostScript-0.06, p5-SOAP-Lite-0.715, p5-SVG-2.53, p5-SVG-Graph-0.04, p5-Scalar-List-Utils-1.25,1, p5-Set-Scalar-1.25, p5-Socket-2.006, p5-Spreadsheet-ParseExcel-0.59,1, p5-Statistics-Descriptive-3.0604, p5-Sub-Exporter-0.984, p5-Sub-Exporter-Progressive-0.001.004, p5-Sub-Install-0.926, p5-Sub-Name-0.05, p5-Task-Weaken-1.04, p5-Text-Iconv-1.7, p5-Text-Shellwords-1.08, p5-Tie-IxHash-1.22, p5-TimeDate-1.20,1, p5-Tree-DAG_Node-1.06, p5-Try-Tiny-0.11, p5-URI-1.60, p5-WWW-RobotRules-6.02, p5-XML-DOM-1.44, p5-XML-DOM-XPath-0.14, p5-XML-Filter-BufferText-1.01, p5-XML-NamespaceSupport-1.11, p5-XML-Parser-2.41, p5-XML-RegExp-0.04, p5-XML-SAX-0.99, p5-XML-SAX-Base-1.08, p5-XML-SAX-Writer-0.53, p5-XML-Twig-3.41, p5-XML-Writer-0.615, p5-XML-XPath-1.13, p5-XML-XPathEngine-0.13, p5-libwww-6.04, p5-libxml-0.08, pango-1.28.4_1, pcre-8.31_1, perl-5.14.2_2, pixman-0.24.2, pkgconf-0.8.9, png-1.5.12, printproto-1.0.5, python27-2.7.3_3, renderproto-0.11.1, xcb-util-0.3.8,1, xcb-util-renderutil-0.3.8, xextproto-7.2.0, xorg-fonts-truetype-7.5.1, xproto-7.0.22
Also listed in: Perl5

p5-bioperl-run-1.6.1_4
Wrapper modules for common bioinformatics tools
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: bitstream-vera-1.10_5, cairo-1.10.2_4,2, encodings-1.0.4,1, expat-2.0.1_2, font-bh-ttf-1.0.3, font-misc-ethiopic-1.0.3, font-misc-meltho-1.0.3, font-util-1.2.0, fontconfig-2.9.0,1, freetype2-2.4.9_1, gamin-0.1.10_4, gd-2.0.35_8,1, gettext-0.18.1.1, gio-fam-backend-2.28.8_1, glib-2.28.8_4, gobject-introspection-0.10.8_2, graphviz-2.28.0_1, jpeg-8_3, kbproto-1.0.5, libICE-1.0.7,1, libSM-1.2.0,1, libX11-1.4.4,1, libXau-1.0.6, libXaw-1.0.9,2, libXdmcp-1.1.0, libXext-1.3.0_1,1, libXft-2.1.14, libXmu-1.1.0,1, libXp-1.0.1,1, libXpm-3.5.9, libXrender-0.9.6, libXt-1.1.1,1, libffi-3.0.9, libfontenc-1.1.0, libiconv-1.14, libltdl-2.4.2, libpthread-stubs-0.3_3, libxcb-1.7, mkfontdir-1.0.6, mkfontscale-1.0.9, mysql-client-5.5.28, p5-AcePerl-1.92_2, p5-Algorithm-C3-0.08, p5-Algorithm-Diff-1.1902, p5-Algorithm-Munkres-0.08, p5-Array-Compare-2.02, p5-Authen-NTLM-1.09, p5-Bio-ASN1-EntrezGene-1.091, p5-Cache-2.04_1, p5-Cache-Cache-1.06, p5-Class-AutoClass-1.01, p5-Class-C3-0.24, p5-Class-Inspector-1.27, p5-Class-Load-0.20, p5-Class-Load-XS-0.05, p5-Clone-0.31, p5-Convert-BinHex-1.119, p5-Convert-Binary-C-0.76, p5-Crypt-RC4-2.02, p5-Crypt-SSLeay-0.64, p5-DBD-mysql-4.021, p5-DBI-1.622, p5-Data-OptList-0.107, p5-Data-Stag-0.11, p5-Devel-GlobalDestruction-0.09, p5-Digest-HMAC-1.03, p5-Digest-Perl-MD5-1.8, p5-Digest-SHA1-2.13, p5-Dist-CheckConflicts-0.02, p5-Email-Date-Format-1.002, p5-Encode-Locale-1.03, p5-Error-0.17018, p5-Eval-Closure-0.08, p5-File-Listing-6.04, p5-File-NFSLock-1.21, p5-GD-2.46_1, p5-GD-SVG-0.33_4, p5-Graph-0.94,1, p5-GraphViz-2.10_1, p5-HTML-Parser-3.69, p5-HTML-Tagset-3.20, p5-HTML-Tree-4.2, p5-HTTP-Cookies-6.01, p5-HTTP-Daemon-6.01, p5-HTTP-Date-6.02, p5-HTTP-Message-6.06, p5-HTTP-Negotiate-6.01, p5-Heap-0.80, p5-IO-Socket-IP-0.17, p5-IO-Socket-SSL-1.76, p5-IO-String-1.08, p5-IO-Tty-1.10, p5-IO-stringy-2.110, p5-IPC-Run-0.92, p5-IPC-ShareLite-0.17, p5-LWP-MediaTypes-6.02, p5-LWP-Protocol-https-6.03, p5-List-MoreUtils-0.33, p5-MIME-Lite-3.02.9, p5-MIME-Tools-5.503,2, p5-MIME-Types-1.35, p5-MRO-Compat-0.11, p5-Mail-Tools-2.11, p5-Math-Derivative-0.01, p5-Math-Random-0.71, p5-Math-Spline-0.01, p5-Module-Build-0.4003, p5-Module-Implementation-0.06, p5-Module-Runtime-0.013, p5-Moose-2.0604, p5-Mozilla-CA-20120823_1, p5-Net-HTTP-6.03_1, p5-Net-SSLeay-1.49, p5-OLE-Storage_Lite-0.19, p5-Package-DeprecationManager-0.13, p5-Package-Stash-0.33, p5-Package-Stash-XS-0.25, p5-Params-Util-1.07, p5-Parse-RecDescent-1.967.009_1, p5-PostScript-0.06, p5-SOAP-Lite-0.715, p5-SVG-2.53, p5-SVG-Graph-0.04, p5-Scalar-List-Utils-1.25,1, p5-Set-Scalar-1.25, p5-Socket-2.006, p5-Spreadsheet-ParseExcel-0.59,1, p5-Statistics-Descriptive-3.0604, p5-Sub-Exporter-0.984, p5-Sub-Exporter-Progressive-0.001.004, p5-Sub-Install-0.926, p5-Sub-Name-0.05, p5-Task-Weaken-1.04, p5-Text-Iconv-1.7, p5-Text-Shellwords-1.08, p5-Tie-IxHash-1.22, p5-TimeDate-1.20,1, p5-Tree-DAG_Node-1.06, p5-Try-Tiny-0.11, p5-URI-1.60, p5-WWW-RobotRules-6.02, p5-XML-DOM-1.44, p5-XML-DOM-XPath-0.14, p5-XML-Filter-BufferText-1.01, p5-XML-NamespaceSupport-1.11, p5-XML-Parser-2.41, p5-XML-RegExp-0.04, p5-XML-SAX-0.99, p5-XML-SAX-Base-1.08, p5-XML-SAX-Writer-0.53, p5-XML-Twig-3.41, p5-XML-Writer-0.615, p5-XML-XPath-1.13, p5-XML-XPathEngine-0.13, p5-bioperl-1.6.1_4, p5-libwww-6.04, p5-libxml-0.08, pango-1.28.4_1, pcre-8.31_1, perl-5.14.2_2, pixman-0.24.2, pkgconf-0.8.9, png-1.5.12, printproto-1.0.5, python27-2.7.3_3, renderproto-0.11.1, xcb-util-0.3.8,1, xcb-util-renderutil-0.3.8, xextproto-7.2.0, xorg-fonts-truetype-7.5.1, xproto-7.0.22
Also listed in: Perl5

paml-4.4c
Phylogenetic Analysis by Maximum Likelihood (PAML)
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: gettext-0.18.1.1, gmake-3.82_1, libiconv-1.14

phd2fasta-0.990622.f
A converter from output files of Phred/Consed to FASTA files
Long description | Sources | Main Web Site
Maintained by: [email protected]

phrap-0.990329
Phrap is a program for assembling shotgun DNA sequence data
Long description | Sources | Main Web Site
Maintained by: [email protected]

phred-0.020425.c
Base calling and quality value assignment on DNA sequencing
Long description | Sources | Main Web Site
Maintained by: [email protected]

phylip-3.69
A Phylogeny Inference Package
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: bash-4.2.37, gettext-0.18.1.1, gmake-3.82_1, kbproto-1.0.5, libICE-1.0.7,1, libSM-1.2.0,1, libX11-1.4.4,1, libXau-1.0.6, libXaw-1.0.9,2, libXdmcp-1.1.0, libXext-1.3.0_1,1, libXmu-1.1.0,1, libXp-1.0.1,1, libXpm-3.5.9, libXt-1.1.1,1, libiconv-1.14, libpthread-stubs-0.3_3, libxcb-1.7, pkgconf-0.8.9, printproto-1.0.5, xextproto-7.2.0, xproto-7.0.22

phyml-20090706
A simple, fast, and accurate algorithm to estimate large phylogenies
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: autoconf-2.69, autoconf-wrapper-20101119, automake-1.12.4, automake-wrapper-20101119, m4-1.4.16_1,1, perl-5.14.2_2

platon-2007.01.09_5
Tool for viewing molecular/crystallographic structures
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: binutils-2.22_3, gcc-4.6.3, gettext-0.18.1.1, gmp-5.0.5, kbproto-1.0.5, libX11-1.4.4,1, libXau-1.0.6, libXdmcp-1.1.0, libiconv-1.14, libpthread-stubs-0.3_3, libxcb-1.7, mpc-0.9, mpfr-3.1.1, pkgconf-0.8.9, xproto-7.0.22

plink-1.07
Whole genome association analysis toolset
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: binutils-2.22_3, blas-3.4.1, gcc-4.6.3, gettext-0.18.1.1, gmake-3.82_1, gmp-5.0.5, lapack-3.4.1, libiconv-1.14, mpc-0.9, mpfr-3.1.1
Also listed in: Science

plinkseq-0.08
Toolset for working with human genetic variation data
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: pkgconf-0.8.9, protobuf-2.4.1
Also listed in: Science

povchem-1.0_7
Simple yet powerful tool to generate POV from a PDB file
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: jbigkit-1.6, jpeg-8_3, kbproto-1.0.5, libX11-1.4.4,1, libXau-1.0.6, libXdmcp-1.1.0, libpthread-stubs-0.3_3, libxcb-1.7, pkgconf-0.8.9, png-1.5.12, povray-3.6.1_10, povray-meta-0.1, svgalib-1.4.3_6, tiff-4.0.2_1, xproto-7.0.22
Also listed in: Graphics

primer3-1.1.4
Primer3 helps to choose primers for PCR reactions
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: gettext-0.18.1.1, gmake-3.82_1, libiconv-1.14

protomol-2.0.3_8
OO, component based, framework for molecular dynamics (MD) simulations
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: damageproto-1.2.1, dri2proto-2.6, expat-2.0.1_2, fixesproto-5.0, freeglut-2.8.0, inputproto-2.0.2, jbigkit-1.6, jpeg-8_3, kbproto-1.0.5, libGL-7.6.1_2, libGLU-7.6.1_1, libICE-1.0.7,1, libSM-1.2.0,1, libX11-1.4.4,1, libXau-1.0.6, libXdamage-1.1.3, libXdmcp-1.1.0, libXext-1.3.0_1,1, libXfixes-5.0, libXi-1.4.5,1, libXmu-1.1.0,1, libXrandr-1.3.2, libXrender-0.9.6, libXt-1.1.1,1, libXxf86vm-1.1.1, libdrm-2.4.17_1, libpciaccess-0.12.1, libpthread-stubs-0.3_3, libxcb-1.7, pciids-20120906, pkgconf-0.8.9, png-1.5.12, randrproto-1.3.2, renderproto-0.11.1, tiff-4.0.2_1, xextproto-7.2.0, xf86vidmodeproto-2.3.1, xproto-7.0.22

psi88-1.0_3
Plotting wavefunctions (molecular orbitals) in 3D
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: binutils-2.22_3, gcc-4.6.3, gettext-0.18.1.1, gmp-5.0.5, libiconv-1.14, mpc-0.9, mpfr-3.1.1

py27-biopython-1.60
Collection of Python modules for bioinformatics
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: binutils-2.22_3, blas-3.4.1, gcc-4.6.3, gettext-0.18.1.1, gmp-5.0.5, lapack-3.4.1, libiconv-1.14, mpc-0.9, mpfr-3.1.1, py27-nose-1.2.1, py27-numpy-1.6.2_1,1, py27-reportlab-1.21.2_3, py27-setuptools-0.6c11_3, python27-2.7.3_3, suitesparse-3.6.1_2
Also listed in: Python

pycogent-1.5.3
A toolkit for statistical analysis of biological sequences
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: binutils-2.22_3, blas-3.4.1, cython-0.17.1, gcc-4.6.3, gettext-0.18.1.1, gmp-5.0.5, lapack-3.4.1, libiconv-1.14, libxml2-2.7.8_5, mpc-0.9, mpfr-3.1.1, mysql-client-5.5.28, pkgconf-0.8.9, postgresql-client-9.0.10, py27-Babel-0.9.6, py27-Jinja2-2.6_1, py27-MarkupSafe-0.15, py27-MySQLdb-1.2.3_2, py27-docutils-0.9.1, py27-nose-1.2.1, py27-numpy-1.6.2_1,1, py27-psycopg2-2.4.5, py27-pygments-1.5, py27-setuptools-0.6c11_3, py27-sphinx-1.1.3_1, py27-sqlalchemy06-0.6.9, py27-sqlite3-2.7.3_2, python27-2.7.3_3, sqlite3-3.7.14.1, suitesparse-3.6.1_2
Also listed in: Python

pyfasta-0.4.5
Fast, memory-efficient, pythonic access to fasta sequence files
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: binutils-2.22_3, blas-3.4.1, gcc-4.6.3, gettext-0.18.1.1, gmp-5.0.5, lapack-3.4.1, libiconv-1.14, mpc-0.9, mpfr-3.1.1, py27-nose-1.2.1, py27-numpy-1.6.2_1,1, py27-setuptools-0.6c11_3, python27-2.7.3_3, suitesparse-3.6.1_2
Also listed in: Python

pymol-1.5.0.1.3978_2
Free and Open-Source molecular modeling system
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: blt-2.4z_7, damageproto-1.2.1, dri2proto-2.6, expat-2.0.1_2, fixesproto-5.0, fontconfig-2.9.0,1, freeglut-2.8.0, freetype2-2.4.9_1, gettext-0.18.1.1, glew-1.9.0, gmake-3.82_1, inputproto-2.0.2, jpeg-8_3, kbproto-1.0.5, libGL-7.6.1_2, libGLU-7.6.1_1, libICE-1.0.7,1, libSM-1.2.0,1, libX11-1.4.4,1, libXau-1.0.6, libXdamage-1.1.3, libXdmcp-1.1.0, libXext-1.3.0_1,1, libXfixes-5.0, libXft-2.1.14, libXi-1.4.5,1, libXmu-1.1.0,1, libXrandr-1.3.2, libXrender-0.9.6, libXt-1.1.1,1, libXxf86vm-1.1.1, libdrm-2.4.17_1, libiconv-1.14, libpciaccess-0.12.1, libpthread-stubs-0.3_3, libxcb-1.7, pciids-20120906, pkgconf-0.8.9, png-1.5.12, py27-Pmw-1.3.2_1, py27-numeric-24.2_3, py27-tkinter-2.7.3_3, python27-2.7.3_3, randrproto-1.3.2, renderproto-0.11.1, tcl-8.5.12_2, tcl-modules-8.5.12_2, tk-8.5.12, xextproto-7.2.0, xf86vidmodeproto-2.3.1, xproto-7.0.22
Also listed in: Python

python-nexus-0.87
A generic nexus file format reader for python
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: gettext-0.18.1.1, libiconv-1.14, py27-setuptools-0.6c11_3, python27-2.7.3_3
Also listed in: Python

rasmol-2.7.2.1.1_3
Fast Molecular Visualization Program
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: gccmakedep-1.0.2, imake-1.0.4,1, inputproto-2.0.2, kbproto-1.0.5, libX11-1.4.4,1, libXau-1.0.6, libXdmcp-1.1.0, libXext-1.3.0_1,1, libXi-1.4.5,1, libpthread-stubs-0.3_3, libxcb-1.7, makedepend-1.0.3,1, perl-5.14.2_2, pkgconf-0.8.9, xextproto-7.2.0, xorg-cf-files-1.0.4, xproto-7.0.22

raster3d-3.0.2_1
A set of tools for generating raster images of proteins and molecules
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: binutils-2.22_3, expat-2.0.1_2, fontconfig-2.9.0,1, freetype2-2.4.9_1, gcc-4.6.3, gd-2.0.35_8,1, gettext-0.18.1.1, gmp-5.0.5, jbigkit-1.6, jpeg-8_3, libiconv-1.14, mpc-0.9, mpfr-3.1.1, pkgconf-0.8.9, png-1.5.12, tiff-4.0.2_1
Also listed in: Graphics

recombine-1.41
A program to fit population models across sites
Long description | Sources | Main Web Site
Maintained by: [email protected]

ruby18-bio-1.4.1
Integrated environment for Bioinformatics written in Ruby
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: ruby-1.8.7.371,1
Also listed in: Ruby

seaview-4.4.0
Multiple DNA/protein sequence alignment editor
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: damageproto-1.2.1, dri2proto-2.6, expat-2.0.1_2, fixesproto-5.0, fltk-1.3.1, fontconfig-2.9.0,1, freetype2-2.4.9_1, gettext-0.18.1.1, gmake-3.82_1, jpeg-8_3, kbproto-1.0.5, libGL-7.6.1_2, libGLU-7.6.1_1, libX11-1.4.4,1, libXau-1.0.6, libXdamage-1.1.3, libXdmcp-1.1.0, libXext-1.3.0_1,1, libXfixes-5.0, libXft-2.1.14, libXinerama-1.1.1,1, libXrender-0.9.6, libXxf86vm-1.1.1, libdrm-2.4.17_1, libiconv-1.14, libpciaccess-0.12.1, libpthread-stubs-0.3_3, libxcb-1.7, pciids-20120906, pdflib-7.0.5_2, pkgconf-0.8.9, png-1.5.12, renderproto-0.11.1, xextproto-7.2.0, xf86vidmodeproto-2.3.1, xineramaproto-1.2.1, xproto-7.0.22

seqan-1.3.1
C++ Sequence Analysis Library
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: binutils-2.22_3, cmake-2.8.9, cmake-modules-2.8.9, gcc-4.6.3, gettext-0.18.1.1, gmp-5.0.5, libiconv-1.14, mpc-0.9, mpfr-3.1.1, python27-2.7.3_3

seqio-1.2.2_1
A set of C functions which can read/write biological sequence files
Long description | Sources | Main Web Site
Maintained by: [email protected]

sim4-2003.09.21
An algorithm for aligning expressed DNA with genomic sequences
Long description | Sources | Main Web Site
Maintained by: [email protected]

ssaha-3.1c_1
Very fast matching and alignment of DNA sequences
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: gettext-0.18.1.1, gmake-3.82_1, libiconv-1.14

tRNAscan-SE-1.23_1
An improved tool for transfer RNA detection
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: perl-5.14.2_2

t_coffee-5.68
A multiple DNA or protein sequence alignment package
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: clustalw-2.1_1

tinker-5.1.09
A general purpose molecular modelling package
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: binutils-2.22_3, gcc-4.6.3, gettext-0.18.1.1, gmp-5.0.5, libiconv-1.14, mpc-0.9, mpfr-3.1.1

treepuzzle-5.2
Maximum likelihood phylogeny reconstruction using quartets
Long description | Sources | Main Web Site
Maintained by: [email protected]

treeviewx-0.5.1_7
A phylogenetic tree viewer
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: ORBit2-2.14.19, atk-2.0.1, bitstream-vera-1.10_5, cairo-1.10.2_4,2, compositeproto-0.4.2, cups-client-1.5.2_2, damageproto-1.2.1, dbus-1.4.14_4, dbus-glib-0.94, dconf-0.5.1_4, dri2proto-2.6, eggdbus-0.6_1, encodings-1.0.4,1, expat-2.0.1_2, fixesproto-5.0, font-bh-ttf-1.0.3, font-misc-ethiopic-1.0.3, font-misc-meltho-1.0.3, font-util-1.2.0, fontconfig-2.9.0,1, freetype2-2.4.9_1, gamin-0.1.10_4, gconf2-2.32.0_3, gdk-pixbuf-2.23.5_3, gettext-0.18.1.1, gio-fam-backend-2.28.8_1, glib-2.28.8_4, gmake-3.82_1, gnome_subr-1.0, gnomehier-2.3_12, gobject-introspection-0.10.8_2, gstreamer-0.10.36, gstreamer-plugins-0.10.36_2,3, gtk-2.24.6_2, gtk-update-icon-cache-2.24.6_1, hicolor-icon-theme-0.12, inputproto-2.0.2, jasper-1.900.1_10, jbigkit-1.6, jpeg-8_3, kbproto-1.0.5, libGL-7.6.1_2, libGLU-7.6.1_1, libICE-1.0.7,1, libIDL-0.8.14_1, libSM-1.2.0,1, libX11-1.4.4,1, libXau-1.0.6, libXcomposite-0.4.3,1, libXcursor-1.1.12, libXdamage-1.1.3, libXdmcp-1.1.0, libXext-1.3.0_1,1, libXfixes-5.0, libXft-2.1.14, libXi-1.4.5,1, libXinerama-1.1.1,1, libXrandr-1.3.2, libXrender-0.9.6, libXt-1.1.1,1, libXv-1.0.6,1, libXxf86vm-1.1.1, libdrm-2.4.17_1, libffi-3.0.9, libfontenc-1.1.0, libgee-0.6.2.1, libiconv-1.14, libmspack-0.3, libpciaccess-0.12.1, libpthread-stubs-0.3_3, libxcb-1.7, libxml2-2.7.8_5, mkfontdir-1.0.6, mkfontscale-1.0.9, orc-0.4.16, pango-1.28.4_1, pciids-20120906, pcre-8.31_1, perl-5.14.2_2, pixman-0.24.2, pkgconf-0.8.9, png-1.5.12, polkit-0.99, python27-2.7.3_3, randrproto-1.3.2, renderproto-0.11.1, shared-mime-info-1.0_1, tiff-4.0.2_1, videoproto-2.3.1, wxgtk2-2.8.12_1, wxgtk2-common-2.8.12_1, wxgtk2-contrib-2.8.12_1, wxgtk2-contrib-common-2.8.12_1, xcb-util-0.3.8,1, xcb-util-renderutil-0.3.8, xextproto-7.2.0, xf86vidmodeproto-2.3.1, xineramaproto-1.2.1, xorg-fonts-truetype-7.5.1, xproto-7.0.22

velvet-1.1.04
Sequence assembler for very short reads
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: gettext-0.18.1.1, gmake-3.82_1, libiconv-1.14, perl-5.14.2_2, python27-2.7.3_3

wise-2.2.0
Intelligent algorithms for DNA searches
Long description | Sources | Main Web Site
Maintained by: [email protected]

wu-blast-2.0_20060322
WU BLAST, a software package for sequence similarity searches
Long description | Sources | Main Web Site
Maintained by: [email protected]

xdrawchem-1.9.9_10
Chemical drawing program
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: boost-libs-1.48.0_1, boost-python-libs-1.48.0, cups-client-1.5.2_2, damageproto-1.2.1, dri2proto-2.6, expat-2.0.1_2, fixesproto-5.0, fontconfig-2.9.0,1, freetype2-2.4.9_1, gettext-0.18.1.1, gmake-3.82_1, icu-4.8.1.1_1, inputproto-2.0.2, jpeg-8_3, kbproto-1.0.5, lcms-1.19_1,1, libGL-7.6.1_2, libGLU-7.6.1_1, libICE-1.0.7,1, libSM-1.2.0,1, libX11-1.4.4,1, libXau-1.0.6, libXaw-1.0.9,2, libXdamage-1.1.3, libXdmcp-1.1.0, libXext-1.3.0_1,1, libXfixes-5.0, libXft-2.1.14, libXi-1.4.5,1, libXinerama-1.1.1,1, libXmu-1.1.0,1, libXp-1.0.1,1, libXpm-3.5.9, libXrender-0.9.6, libXt-1.1.1,1, libXxf86vm-1.1.1, libdrm-2.4.17_1, libiconv-1.14, libmng-1.0.10_2, libpciaccess-0.12.1, libpthread-stubs-0.3_3, libxcb-1.7, libxml2-2.7.8_5, nas-1.9.3, openbabel-2.2.3, pciids-20120906, pkgconf-0.8.9, png-1.5.12, printproto-1.0.5, python27-2.7.3_3, qt-3.3.8_14, renderproto-0.11.1, xextproto-7.2.0, xf86vidmodeproto-2.3.1, xineramaproto-1.2.1, xproto-7.0.22

xmolwt-0.7_4
Calculate formula weight and percent of each element for a given formula
Long description | Sources | Main Web Site
Maintained by: [email protected]
Requires: gettext-0.18.1.1, glib-1.2.10_13, gmake-3.82_1, gtk-1.2.10_22, inputproto-2.0.2, kbproto-1.0.5, libICE-1.0.7,1, libSM-1.2.0,1, libX11-1.4.4,1, libXau-1.0.6, libXdmcp-1.1.0, libXext-1.3.0_1,1, libXi-1.4.5,1, libiconv-1.14, libpthread-stubs-0.3_3, libxcb-1.7, pkgconf-0.8.9, xextproto-7.2.0, xproto-7.0.22

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